“DIY-science” Workshop

Every year team Vilnius-Lithuania is trying to find more and more attractive ways to reach out to the general public and reveal the fascinating world of life sciences to them. With the intention to prove to the lay public that everyone has potential to become a scientist and that research does not necessarily require an advanced laboratory, we organized a unique public “DIY-science” workshop as a part of European Biotech Week in Vilnius.

This year we collaborated with an interdisciplinary artist Mindaugas Gapševičius who helped us pass on our knowledge to the non-scientific audience. Mindaugas was interested in various laboratory methods performed using DIY equipment. Therefore we invited him to visit our laboratory where wet lab team members instructed him on making DNA samples, showed the equipment in our laboratory, and compared it with DIY devices. After work in the lab and a lot of discussions with the artist, an idea to organise a specific workshop was born.

Typically workshops let participants feel more free while asking questions or carrying out experiments that they have never done before. Therefore more knowledge and personal experience is gained in a limited amount of time. While comparing concepts of the event, everyone agreed that it was important to adjust the theme of the workshop to some common everyday life issue that people could relate to. We have analysed what phenotypes or diseases are common and still raise lots of questions about their genesis to the general public and eventually chose to work on lactose intolerance. It is a frequent problem with an approximate 65% prevalence in population. Finally, having everything set up, 20 people from the lay public with background in arts, IT, medicine, and also life sciences were invited to test, using DIY tools, whether they have a susceptibility for lactose intolerance or not.

The framework also includes a possibility of adding a selection system that reduces the usage of antibiotics (only 1 antibiotic for up to 5 different plasmids!) and an active partitioning system to make sure that low copy number plasmid groups are not lost during the division.

EPE FOTO

At the beginning of the workshop we introduced people to the main aspects of DNA structure, gene regulation, and how it determines lactose intolerance. We explained that even a single nucleotide polymorphism (SNP) in a particular site can lead to a decreased expression of lactase (LCT) gene which results in reduced production of lactase enzyme after infancy occurs. Therefore people were able to understand that the root of disturbed lactose breakdown lies in genes and the expression of specific protein.

During the practice session participants were taught how to prepare samples for polymerase chain reaction (PCR) from their saliva and some additional reagents. The PCR reaction that we together performed amplified a specific segment of sample DNA, in our case - the LCT gene’s regulator. After PCR and DNA electrophoresis were done, people had an opportunity to gain some knowledge and skills on DNA fingerprinting. This method enabled people to observe variations in the LCT gene’s regulator. The more topics were covered, the more questions were raised by our workshop participants. They developed into discussions about genetic tests and their applications, as well as limitations of DIY biology and home-made laboratories.

What was really exceptional about this workshop, is that we have used only homemade equipment: thermocycler, centrifuge, and gel electrophoresis chamber to perform all reactions and procedures. Every device was handmade by household tools, and people were able to carry all experiments not in a laboratory setting, but simply in an art gallery. These aspects revealed the abilities and possibilities to utilize DIY biology. Due to the fact that this equipment was made using household tools (e.g., computer and an air cooler), we managed to convince participants that even non-scientific people could perform significant experiments and find interesting things about themselves outside the laboratory. This informal environment helped participants feel more comfortable to ask questions they were concerned about.

Although designing a homemade thermocycler on one's own is rather simple, some more elaborate competences to programme an Arduino microcontroller are needed. Workshop’s participants, those you knew Python, had an opportunity to help us with programming it, while others could observe, ask, and learn the most basic principles of programming.

As the idea of “DIY-science” workshop won lots of recognition and appreciation from the public, we want to share some tutorials, an open source Arduino microcontroller operation code, and a principal scheme of thermocycler device which might be helpful to invoke and improve this workshop idea among other iGEM teams in the near future.

Applications

Everyday lab work

A multi-plasmid system that is easy to assemble and control. With our framework the need to limit your research to a particular plasmid copy number just because there are not enough right replicons to choose from, is eliminated. With SynORI you can easily create a vector with a desired copy number that suits your needs.

Biological computing

The ability to choose a wide range of copy number options and their control types will make the synthetic biology engineering much more flexible and predictable. Introduction of plasmid copy number regulation is equivalent to adding a global parameter to a computer system. It enables the coordination of multiple gene group expression.

Smart assembly of large protein complexes

The co-expression of multi-subunit complexes using different replicons brings incoherency to an already chaotic cell system. This can be avoided by using SynORI, as in this framework every plasmid group uses the same type of control, and in addition can act in a group-specific manner.

Metabolic engineering

A big challenge for heterologous expression of multiple gene pathways is to accurately adjust the levels of each enzyme to achieve optimal production efficiency. Precise promoter tuning in transcriptional control and synthetic ribosome binding sites in translational control are already widely used to maintain expression levels. In addition to current approaches, our framework allows a simultaneous multiple gene control. Furthermore, an inducible regulation that we offer, can make the search for perfect conditions a lot easier.

Species sign in ODE system	Species	Initial concentration (M)
A	pDNA+RNA I+RNAII early	0
B	pDNA+RNA II short	0
RNAI	RNA I	1E-6
D	pDNA+RNA II long	0
E	pDNA+RNAII primer	0
F	RNA II long	0
G	pDNA	4E-8*
H	pDNA+RNA II+RNA I late	0
RNA II	RNA II	0
J	RNAI+RNAII	0